The eight-woman, four-man panel in the 14-week case took six days to decide that Lay, 64, was guilty of all six counts of fraud and conspiracy. Skilling, 52, was convicted of all securities, wire fraud and conspiracy counts but not of charges related to insider trading, ABC News and the Wall Street Journal reported.
Both men are expected to appeal.
During the trial Skilling and his lawyers argued that there had not been any widespread fraud; Lay and his lawyers argued that he was unaware of accounting details that may have been amiss.
One of the government's top witnesses was former Enron financial head Andrew Fastow who pleaded guilty in the case and testified against his former bosses.
The case stems from Enron's December 2001 collapse as investors bailed out on reports the giant energy trader had cooked its books to hide massive losses and maintain its share price.
After the fall, the federal government formed a task force to untangle the mess and, to date, about 30 people have been criminally charged and 12 have pleaded guilty to crimes.